I agree on the Matrix movies, but they had much more of a free pass already, because the core concepts are so flexible.
Did you have some specific examples in mind? I still feel as though 2001, excluding its ending, stayed much further away from speculative topics of theoretical physics than did Interstellar (which in fact has explicit references, in its dialogue, to "the bulk" -- a term from brane cosmology; see http://en.wikipedia.org/wiki/Brane_cosmology).
Maybe 2001 just did a better job than Interstellar of drawing lines for the audience between "known science" and "alien technology so advanced it looks like magic." So that 2001 still has a great reputation for scientific accuracy despite the fact it contains elements at least as fantastic as Interstellar does.
That is true, but it is not enough. A lot of Interstellar criticism comes from the fact that events described as scientifically feasible were in fact not. I will not describe what particular problems can be found in Interstellar because other posts in this thread already touched virtually every possible issue.